The optimal solution I've come up with is to use the two keys adjacent to the space bar (typically Alt, but actually Command on the Apple keyboard I generally use) as Control, since that's easily the most important modifier key, so it should be the easiest to access. This makes C-w, C-s, C-r, C-a, C-e, C-p, C-o, C-j, C-l and so on very, very comfortable compared to the corner positioning. As far as I know, this is the way many keyboards were before the extended IBM PC keyboard came up with its insane control key positioning. (My comfort with these keys may also be linked to my use of Macs and ubiquitous command-key shortcuts before I switched to Ubuntu. Ironically, Emacs is much more comfortable now in Ubuntu than it ever was on my Mac, because I can use the most readily accessible modifier key as God intended, rather than the third-tier relegated modifier that Control is on the Mac.)
The two keys adjacent to the new Control keys (ie. 2 away from the spacebar) then become the Alt keys. Whatever is left over (the original ctrl keys, plus Caps Lock and any silly Windows keys left over) can be bound to Super, which is useful for window manager shortcuts so that they don't clobber emacs/bash/screen bindings.
These changes are trivially easy to put in a simple .Xmodmap file to load whenever you log in, and copy to all the other computers you have to use regularly. If you're using Windows, I guess you may have to fiddle with the registry, but it would be worth it.